Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms

Abstract

The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.

Figure 1

Intersection between the adoption of microbial chassis and the fields of metabolic engineering and synthetic biology, as reflected in the relevant literature since 1961 up to date. The diagram indicates the number of times that the words ‘Metabolic Engineering’ (blue), ‘Synthetic Biology’ (green) and ‘chassis’ (yellow) have been used as keywords in research and review articles in the field literature over the years (source: PubMed, accessed in May 2018). Note that the scale is different for ‘chassis’ (indicated to the right of the diagram) and both ‘Metabolic Engineering’ and ‘Synthetic Biology’ (indicated to the left of the diagram).

Figure 2

Proposed chart for the development of a bacterial chassis for metabolic engineering, indicating the key steps required for domestication of a potentially interesting wild‐type strain. The entire process builds upon six main interconnected aspects, which cover the whole range between gaining fundamental insight into functional genomics and physiology of the strain at stake and the design and adoption of dedicated synthetic biology tools. Although there is a structure to be followed along the process (that usually starts with the sequencing and expert annotation of the genome and a thorough physiological characterization), the steps indicated in the chart are not necessarily sequential in nature.

Figure 3

Functional relationship between intended industrially relevant practical applications and different bacterial chassis of choice, depending on some key physiological and metabolic features they present. For the sake of simplicity, only some selected applications are shown along with the bacterial species that could be adopted as the starting point for robust chassis design and construction. Note that, given the characteristics of some of these bacterial species, they could potentially fulfil more than one application.

Figure 4

Some of the challenges ahead for developing functional bacterial chassis for metabolic engineering. Effective bioproduction could only be achieved by overcoming the current hurdles of genetic and genomic instability (e.g. leading to alteration or loss of production phenotypes), phenotypic variability across individual cells in the microbial population, and the inevitable interactions between metabolic implants and the extant biochemistry of the bacterial chassis. The way forward to tackle these issues requires the combination of robust in silico predictions and in‐depth experimental validation, if possible under conditions compatible with industrial production.